MolNFT v1 · #140165 · protein
Crystal structure of AL2 pal domain in complex with ATRING1A proximal site
5Y21 · Phd finger protein alfin-like 2: “Crystal structure of AL2 pal domain in complex with ATRING1A proximal site”. X-ray diffraction, 5 pockets (best druggability 0.79). MolNFT v1 #140165 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5Y21
- Type
- protein
- Length
- 283 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein alfin-like 2; ATRING1A proximal binding site peptide
- UniProt
- Q9SRM4, F4K8U4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phd finger protein alfin-like 2 | protein | 131 | 53% helix, 8% strand | Q9SRM4 |
| C | ATRING1A proximal binding site peptide | protein | 12 | 0% helix, 17% strand | F4K8U4 |
| D | ATRING1A proximal binding site peptide | protein | 9 | 0% helix, 22% strand | F4K8U4 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.79 | 0.97 | 28 | empty |
| 2 | 57 | 0.71 | 0.98 | 19 | empty |
| 3 | 103 | 0.42 | 0.77 | 19 | empty |
| 4 | 94 | 0.36 | 0.75 | 19 | empty |
| 5 | 61 | 0.30 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1583 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 410 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 354 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 333 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5Y21 · Crystal structure of AL2 PAL domain in complex with AtRing1a proximal site · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SRM4 · AlphaFold monomer V2.0 prediction for phd finger protein alfin-like 2 (Q9SRM4) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9SRM4
- Every structure of UniProt F4K8U4
- Elsewhere: RCSB PDB 5Y21 · PDBe 5Y21 · UniProt Q9SRM4 · UniProt F4K8U4
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